Posts
Jun, 3
A GPU-accelerated Boundary Element Method and Vortex Particle Method
Vortex particle methods, when combined with multipole-accelerated boundary element methods (BEM), become a complete tool for direct numerical simulation (DNS) of internal or external vortex-dominated flows. In previous work, we presented a method to accelerate the vorticity-velocity inversion at the heart of vortex particle methods by performing a multipole treecode N-body method on parallel graphics […]
Jun, 3
Bayesian Sparsity-Path-Analysis of Genetic Association Signal using Generalized t Priors
We explore the use of generalized t priors on regression coefficients to help understand the nature of association signal within "hit regions" of genome-wide association studies. The particular generalized t distribution we adopt is a Student distribution on the absolute value of its argument. For low degrees of freedom we show that the generalized t […]
Jun, 2
High Performance Computational Systems Biology, HiBi 2011
Special session of 9th International Conference on Computational Methods in Systems Biology (CMSB 2011) Computational methods in biology enable the systematic study of the complex interactions that characterize biological systems. Mathematical modelling is a necessary tool to unambiguously represent the information about the behaviour of the considered system and to enable sophisticated predictive analysis. One […]
Jun, 2
The 10th International Symposium on Parallel and Distributed Computing, ISPDC 2011
The 10th International Symposium on Parallel and Distributed Computing (ISPDC 2011) will take place between July 6th and 8th, 2011, in Cluj-Napoca, Romania. This year’s edition is organized by the Computer Science Department of the Technical University of Cluj-Napoca. It will feature keynote presentations and oral paper presentations, as well as several special sessions and […]
Jun, 2
CUDA-based Signed Distance Field Calculation for Adaptive Grids
We present a simple yet robust signed distance field (SDF) generator based on recent GPU architectures. In our approach, the squared Euclidean distance is calculated for each triangle face in parallel, and then an optimized stream reduction process is used to find the shortest distance. During this process, the stream reduction operation acts like a […]
Jun, 2
Sparse matrix computations on manycore GPU’s
Modern microprocessors are becoming increasingly parallel devices, and GPUs are at the leading edge of this trend. Designing parallel algorithms for manycore chips like the GPU can present interesting challenges, particularly for computations on sparse data structures. One particularly common example is the collection of sparse matrix solvers and combinatorial graph algorithms that form the […]
Jun, 2
A Reverse-Projecting Pixel-Level Painting Algorithm
Traditional Texturing using a set of two dimensional image maps is an established and widespread practice. However, it is difficult to parameterize a model in texture space, particularly with representations such as implicit surfaces, subdivision surfaces, and very dense or detailed polygonal meshes. Based on an adaptive octree textures definition, this paper proposes a direct […]
Jun, 2
Massively Parallel Finite Element Simulator for Full-Chip STI Stress Analysis
In modern integrated circuit (IC) designs with feature size finer than 90nm, the stress among different material layers is playing an important role in determining device performance. The stress can be classified into two categories, stress deliberately introduced during semiconductor process, and stress unintentionally formed through the synergy of different processing steps. Among different types […]
Jun, 2
RNA secondary structure prediction using dynamic programming algorithm – A review and proposed work
Ribonucleic acid (RNA) plays a fundamental and important role in cellular life forms and their function is directly related to their structure. RNA secondary structure prediction is a significant area of study for many scientists seeking insights into potential drug interactions or innovative new treatment methodologies. Predicting structure can overcome many issues related with physical […]
Jun, 2
Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit
All-atom normal mode analysis (NMA) is an efficient way to predict the collective motions in a given macromolecule, which is essential for the understanding of protein biological function and drug design. However, the calculations are limited in time scale mainly because the required diagonalization of the Hessian matrix by Householder-QR transformation is a computationally exhausting […]
Jun, 2
MapCG: writing parallel program portable between CPU and GPU
Graphics Processing Units (GPU) have been playing an important role in the general purpose computing market recently. The common approach to program GPU today is to write GPU specific code with low level GPU APIs such as CUDA. Although this approach can achieve very good performance, it raises serious portability issues: programmers are required to […]
Jun, 2
Acceleration of LOD-FDTD Method Using Fundamental Scheme on Graphics Processor Units
This letter presents the acceleration of locally one-dimensional finite-difference time-domain (LOD-FDTD) method using fundamental scheme on graphics processor units (GPUs). Compared to the conventional scheme, the fundamental LOD-FDTD (denoted as FLOD-FDTD) scheme has its right-hand sides cast in the simplest form without involving matrix operators. This leads to a substantial reduction in floating-point operations as […]
